Contacts of the helix formed by residues 66 - 86 (chain A) in PDB entry 2Z98
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 2.7 28.2 + - + +
65A LEU* 1.3 74.4 - - - +
67A PRO* 1.4 72.9 - - - +
68A ARG* 3.5 2.4 + - - -
69A GLN* 2.8 38.3 + - - +
70A GLN* 2.9 22.1 + - - +
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU 4.6 1.3 - - - +
66A THR* 1.4 83.7 - - - +
68A ARG* 1.3 56.7 + - - +
70A GLN* 3.1 16.2 + - - +
71A GLU* 2.9 41.9 + - - +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 4.9 6.7 - - - +
49A VAL 4.8 2.2 + - - -
51A ASP* 3.0 33.3 + - - -
53A GLU* 2.7 42.1 + - - +
54A LEU* 3.9 27.6 - - + +
66A THR* 3.1 5.6 + - - +
67A PRO* 1.3 76.5 - - + +
69A GLN* 1.3 66.2 + - - +
71A GLU* 3.4 10.0 + - - +
72A ALA* 3.0 25.3 + - - +
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 2.9 44.8 + - + +
54A LEU* 4.5 1.3 - - - -
56A GLY* 3.9 7.7 - - - -
57A ALA* 3.2 33.6 - - + +
65A LEU* 3.4 20.4 - - + +
66A THR* 2.8 51.7 + - - +
68A ARG* 1.3 77.0 - - - +
70A GLN* 1.4 62.7 + - - +
72A ALA* 4.5 1.8 - - - -
73A LEU* 3.0 21.7 + - - +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.2 40.0 + - + +
66A THR 2.9 17.6 + - - +
67A PRO* 3.4 16.3 - - - +
69A GLN* 1.4 75.4 - - - +
71A GLU* 1.3 65.3 + - + +
73A LEU* 3.3 5.0 + - - +
74A ALA* 3.0 24.6 + - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO* 2.9 28.9 + - - +
68A ARG* 3.9 7.7 - - - +
69A GLN 3.3 0.2 - - - -
70A GLN* 1.3 78.2 - - + +
72A ALA* 1.4 55.3 + - - +
74A ALA* 3.3 6.4 + - - +
75A LEU* 2.9 29.7 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 5.3 4.0 - - + -
54A LEU* 3.6 36.8 - - + -
57A ALA* 4.6 3.6 - - + -
58A LEU* 4.2 6.5 - - + +
68A ARG 3.0 17.6 + - - +
69A GLN* 3.8 4.0 - - - +
71A GLU* 1.4 75.9 - - - +
73A LEU* 1.3 57.1 + - - +
75A LEU* 3.8 8.0 - - - +
76A SER* 2.9 30.1 + - - -
110A LEU* 4.4 8.1 - - + +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 3.7 22.7 - - - +
58A LEU* 4.1 12.0 - - + +
65A LEU* 3.8 16.4 - - + -
69A GLN 3.0 17.6 + - - +
70A GLN* 3.7 5.8 - - + +
72A ALA* 1.3 76.4 - - - +
74A ALA* 1.3 58.0 + - - +
76A SER* 3.3 2.4 + - - -
77A ASP* 2.9 44.0 + - - +
113A ARG* 3.5 33.4 - - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLN 3.0 16.7 + - - +
71A GLU* 3.7 6.7 - - - +
73A LEU* 1.3 78.8 - - - +
75A LEU* 1.3 56.9 + - - +
77A ASP* 3.5 9.8 + - - +
78A GLU* 3.0 28.3 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 5.1 4.3 - - - +
46A PRO 5.5 0.9 - - - +
47A ILE* 4.2 15.7 - - + -
48A PRO* 3.6 32.5 - - + -
71A GLU 2.9 18.1 + - - +
72A ALA* 3.8 5.8 - - - +
74A ALA* 1.3 72.5 - - - +
76A SER* 1.4 65.6 + - - +
78A GLU* 3.3 22.7 + - - +
79A LEU* 2.9 44.4 + - + +
110A LEU* 3.8 14.8 - - + -
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.0 12.8 - - - -
72A ALA 2.9 18.2 + - - -
73A LEU 3.6 4.3 - - - -
75A LEU* 1.4 78.0 - - - +
77A ASP* 1.3 63.2 + - - +
79A LEU* 3.3 3.1 + - - +
80A ILE* 2.9 30.0 + - - +
110A LEU* 2.7 39.1 + - - +
113A ARG* 2.9 27.7 + - - -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 2.9 33.3 + - - +
74A ALA* 3.7 8.9 - - - +
76A SER* 1.3 78.6 - - - +
78A GLU* 1.3 56.7 + - - +
80A ILE* 3.4 5.6 + - - +
81A ALA* 2.9 31.1 + - - +
113A ARG* 2.9 27.7 + - - +
116A VAL* 5.9 1.6 - - - +
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.1 28.6 + - - +
74A ALA 3.0 17.6 + - - +
75A LEU* 3.5 23.7 - - - +
76A SER 3.2 0.2 - - - -
77A ASP* 1.3 76.5 - - - +
79A LEU* 1.4 62.7 + - - +
81A ALA* 3.3 4.9 + - - +
82A GLU* 2.9 25.9 + - + +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.5 46.2 - - - +
47A ILE* 4.0 24.2 - - + -
75A LEU* 2.9 31.7 + - + +
76A SER 3.8 3.6 - - - +
78A GLU* 1.4 72.6 - - + +
80A ILE* 1.3 56.8 + - - +
82A GLU* 3.3 6.7 + - - +
83A LEU* 3.0 27.2 + - - +
107A TYR* 4.0 25.1 + - + -
110A LEU* 4.1 29.4 - - + -
111A VAL* 4.0 15.3 - - + -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A SER* 2.9 26.6 + - - +
77A ASP* 3.9 5.2 - - - +
79A LEU* 1.3 73.7 - - - +
81A ALA* 1.3 63.6 + - - +
83A LEU* 3.2 7.1 + - + +
84A LYS* 2.9 42.3 + - + +
110A LEU 3.9 0.7 - - - +
111A VAL* 3.7 28.9 - - + +
113A ARG* 3.6 37.0 - - + +
116A VAL* 3.9 25.1 - - + -
117A THR* 3.7 19.3 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP 2.9 19.2 + - - +
78A GLU* 3.8 5.8 - - - +
80A ILE* 1.3 80.4 - - - +
82A GLU* 1.3 62.1 + - - +
84A LYS* 3.4 6.3 + - - +
85A ALA* 2.9 24.8 + - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.7 32.1 - - + +
6A LEU* 4.8 1.2 - - - +
38A THR* 4.2 12.0 - - - +
40A ARG* 2.8 47.7 + - - +
78A GLU* 2.9 18.7 + - + +
79A LEU* 3.6 7.6 - - - +
81A ALA* 1.3 76.8 - - - +
83A LEU* 1.4 61.2 + - - +
85A ALA* 3.1 9.5 + - - -
86A HIS* 2.8 36.0 + - + -
107A TYR* 5.0 2.1 - - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.2 8.3 - - + +
6A LEU* 5.5 0.4 - - + -
79A LEU 3.0 17.0 + - - +
80A ILE* 3.7 5.6 - - - +
82A GLU* 1.4 75.9 - - - +
84A LYS* 1.3 63.2 + - + +
85A ALA 3.3 0.3 + - - -
86A HIS* 3.4 15.9 + - - +
89A ILE* 3.8 37.1 - - + +
107A TYR* 3.9 20.4 - - + +
111A VAL* 3.6 30.5 - - + -
117A THR* 5.3 1.8 - - + -
129A VAL* 4.3 20.9 - - + -
132A LYS* 3.6 5.8 - - - -
163A ILE* 4.0 17.3 - - + -
165A ILE* 4.4 8.3 - - + -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 2.9 36.9 + - + +
81A ALA* 4.0 5.4 - - - +
83A LEU* 1.3 77.6 - - + +
85A ALA* 1.3 56.6 - - - +
116A VAL* 2.8 34.4 + - - +
128A LEU* 4.5 12.8 + - - +
129A VAL* 4.3 29.2 - - + -
132A LYS* 2.8 27.9 + - - +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 3.6 24.3 - - + +
81A ALA 2.9 17.8 + - - +
82A GLU* 3.1 9.1 + - - +
84A LYS* 1.3 75.8 - - - +
86A HIS* 1.3 66.2 + - + +
87A ASP* 4.3 2.9 + - - +
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 3.7 32.5 + - + +
3A VAL 3.4 27.1 - - - -
4A LEU* 3.5 20.8 - - + +
36A GLU 4.7 1.0 + - - -
38A THR* 2.9 30.3 + - + -
82A GLU* 2.8 42.0 + - + +
83A LEU 3.4 2.2 + - - +
84A LYS 3.3 0.6 - - - -
85A ALA* 1.3 87.5 - - + +
87A ASP* 1.3 59.6 + - - +
88A VAL 3.7 0.2 - - - -
89A ILE* 3.8 10.6 - - + +
132A LYS* 2.7 33.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il